Magnesium in PDB 6p63: Wild-Type Nis Synthetase Desd Bound to Amp and Substrate Analog Cadaverine

The structure of Wild-Type Nis Synthetase Desd Bound to Amp and Substrate Analog Cadaverine, PDB code: 6p63 was solved by K.M.Hoffmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.83 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	98.430, 74.240, 183.170, 90.00, 94.70, 90.00
R / Rfree (%)	19.6 / 22.8

The binding sites of Magnesium atom in the Wild-Type Nis Synthetase Desd Bound to Amp and Substrate Analog Cadaverine (pdb code 6p63). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Wild-Type Nis Synthetase Desd Bound to Amp and Substrate Analog Cadaverine, PDB code: 6p63:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Wild-Type Nis Synthetase Desd Bound to Amp and Substrate Analog Cadaverine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Wild-Type Nis Synthetase Desd Bound to Amp and Substrate Analog Cadaverine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:38.0 occ:1.00 OE1 A:GLU445 2.1 14.0 1.0 O3P A:AMP601 2.2 29.0 1.0 OD1 A:ASN446 2.6 9.9 1.0 OD2 A:ASP463 3.0 17.9 1.0 CD A:GLU445 3.1 13.7 1.0 O A:HOH840 3.2 16.2 1.0 OE2 A:GLU445 3.4 14.0 1.0 P A:AMP601 3.5 31.1 1.0 CG A:ASP463 3.5 18.8 1.0 CB A:ASP463 3.5 16.5 1.0 CG A:ASN446 3.7 9.7 1.0 O5' A:AMP601 3.8 28.6 1.0 O1P A:AMP601 4.0 29.0 1.0 C5' A:AMP601 4.1 26.9 1.0 CB A:SER278 4.2 10.3 1.0 ND2 A:ASN446 4.2 9.6 1.0 CG A:GLU445 4.5 12.8 1.0 OD1 A:ASP463 4.5 22.5 1.0 O A:GLU445 4.6 10.1 1.0 NZ A:LYS462 4.7 13.9 1.0 O2P A:AMP601 4.7 29.7 1.0 CE1 A:HIS443 4.8 11.8 1.0 OG A:SER278 4.8 10.8 1.0 C A:GLU445 4.9 10.5 1.0 C4' A:AMP601 4.9 24.6 1.0 CA A:ASP463 4.9 15.4 1.0 CB A:ASN446 5.0 9.5 1.0

Magnesium binding site 2 out of 4 in the Wild-Type Nis Synthetase Desd Bound to Amp and Substrate Analog Cadaverine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Wild-Type Nis Synthetase Desd Bound to Amp and Substrate Analog Cadaverine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:29.0 occ:1.00 O1P B:AMP601 1.9 25.8 1.0 OD1 B:ASN446 2.3 9.0 1.0 OE1 B:GLU445 2.3 15.6 1.0 OD2 B:ASP463 2.8 20.7 1.0 P B:AMP601 3.2 27.9 1.0 CG B:ASN446 3.3 8.5 1.0 CG B:ASP463 3.4 18.8 1.0 CD B:GLU445 3.4 15.1 1.0 CB B:ASP463 3.4 16.6 1.0 O B:HOH900 3.7 13.5 1.0 O3P B:AMP601 3.7 30.3 1.0 ND2 B:ASN446 3.8 7.9 1.0 O5' B:AMP601 3.8 24.0 1.0 OE2 B:GLU445 3.9 19.3 1.0 C5' B:AMP601 4.1 23.7 1.0 O2P B:AMP601 4.4 30.0 1.0 CE1 B:HIS443 4.4 10.6 1.0 OD1 B:ASP463 4.5 23.6 1.0 CB B:ASN446 4.6 8.7 1.0 CB B:SER278 4.7 11.3 1.0 CG B:GLU445 4.7 13.8 1.0 OE2 B:GLU467 4.7 17.3 1.0 O B:GLU445 4.7 10.5 1.0 CA B:ASN446 4.8 9.0 1.0 CA B:ASP463 4.9 15.7 1.0 C B:GLU445 4.9 10.2 1.0 NE2 B:HIS443 4.9 10.1 1.0 N B:ASN446 5.0 9.1 1.0

Magnesium binding site 3 out of 4 in the Wild-Type Nis Synthetase Desd Bound to Amp and Substrate Analog Cadaverine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Wild-Type Nis Synthetase Desd Bound to Amp and Substrate Analog Cadaverine within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:29.7 occ:1.00 O1P C:AMP602 1.9 24.0 1.0 OE1 C:GLU445 2.3 19.8 1.0 O C:HOH737 2.4 21.1 1.0 OD1 C:ASN446 2.4 10.6 1.0 OD2 C:ASP463 2.7 15.8 1.0 P C:AMP602 3.0 24.1 1.0 CG C:ASP463 3.2 16.3 1.0 O3P C:AMP602 3.3 27.1 1.0 CB C:ASP463 3.4 15.1 1.0 CD C:GLU445 3.4 17.6 1.0 CG C:ASN446 3.5 10.3 1.0 O5' C:AMP602 3.7 22.9 1.0 O C:HOH703 3.7 25.6 1.0 OE2 C:GLU445 3.8 18.1 1.0 O C:HOH863 3.8 12.1 1.0 ND2 C:ASN446 3.9 10.3 1.0 C5' C:AMP602 4.2 22.5 1.0 O C:HOH870 4.3 14.2 1.0 OD1 C:ASP463 4.3 20.5 1.0 O2P C:AMP602 4.4 28.2 1.0 CE1 C:HIS443 4.5 11.5 1.0 CB C:SER278 4.6 9.8 1.0 OE2 C:GLU467 4.7 18.2 1.0 CG C:GLU445 4.7 15.8 1.0 CB C:ASN446 4.8 10.3 1.0 CA C:ASP463 4.8 14.4 1.0 O C:GLU445 4.9 12.2 1.0 NE2 C:HIS443 4.9 11.0 1.0 CA C:ASN446 5.0 10.3 1.0

Magnesium binding site 4 out of 4 in the Wild-Type Nis Synthetase Desd Bound to Amp and Substrate Analog Cadaverine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Wild-Type Nis Synthetase Desd Bound to Amp and Substrate Analog Cadaverine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:29.4 occ:1.00 O2P D:AMP601 2.1 28.7 1.0 OE1 D:GLU445 2.2 11.2 1.0 OD1 D:ASN446 2.5 7.2 1.0 OD2 D:ASP463 2.9 19.5 1.0 CD D:GLU445 3.2 11.3 1.0 P D:AMP601 3.3 25.4 1.0 CG D:ASP463 3.4 19.4 1.0 O D:HOH875 3.4 15.0 1.0 CB D:ASP463 3.4 16.6 1.0 OE2 D:GLU445 3.5 13.5 1.0 CG D:ASN446 3.6 7.4 1.0 O1P D:AMP601 3.7 30.2 1.0 O5' D:AMP601 3.8 26.6 1.0 ND2 D:ASN446 4.1 7.2 1.0 C5' D:AMP601 4.2 23.7 1.0 O D:HOH860 4.3 16.2 1.0 CB D:SER278 4.4 10.6 1.0 OD1 D:ASP463 4.5 23.8 1.0 O3P D:AMP601 4.6 30.7 1.0 CG D:GLU445 4.6 10.7 1.0 O D:GLU445 4.7 8.8 1.0 CE1 D:HIS443 4.7 10.3 1.0 CA D:ASP463 4.8 15.4 1.0 CB D:ASN446 4.9 7.5 1.0 OE2 D:GLU467 4.9 16.7 1.0 C D:GLU445 5.0 9.0 1.0

K.M.Hoffmann, C.Amendola, E.Goncuian, K.Karimi, J.Kovak, Y.Mojab, G.Prussia. Structure of Iterative Nis Synthetase Desd To Be Published.